OOPSE/libmdtools/NPTf.cpp

#include <math.h>

#include "MatVec3.h"
#include "Atom.hpp"
#include "SRI.hpp"
#include "AbstractClasses.hpp"
#include "SimInfo.hpp"
#include "ForceFields.hpp"
#include "Thermo.hpp"
#include "ReadWrite.hpp"
#include "Integrator.hpp"
#include "simError.h"

#ifdef IS_MPI
#include "mpiSimulation.hpp"
#endif

// Basic non-isotropic thermostating and barostating via the Melchionna
// modification of the Hoover algorithm:
//
//    Melchionna, S., Ciccotti, G., and Holian, B. L., 1993,
//       Molec. Phys., 78, 533.
//
//           and
//
//    Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.

template<typename T> NPTf<T>::NPTf ( SimInfo *theInfo, ForceFields* the_ff):
  T( theInfo, the_ff )
{
  GenericData* data;
  DoubleArrayData * etaValue;
  vector<double> etaArray;
  int i,j;

  for(i = 0; i < 3; i++){
    for (j = 0; j < 3; j++){

      eta[i][j] = 0.0;
      oldEta[i][j] = 0.0;
    }
  }


  if( theInfo->useInitXSstate ){
    // retrieve eta array from simInfo if it exists
    data = info->getProperty(ETAVALUE_ID);
    if(data){
      etaValue = dynamic_cast<DoubleArrayData*>(data);
      
      if(etaValue){
        etaArray = etaValue->getData();
        
        for(i = 0; i < 3; i++){
          for (j = 0; j < 3; j++){
            eta[i][j] = etaArray[3*i+j];
            oldEta[i][j] = eta[i][j];
          }
        }
      }
    }
  }

}

template<typename T> NPTf<T>::~NPTf() {

  // empty for now
}

template<typename T> void NPTf<T>::resetIntegrator() {

  int i, j;

  for(i = 0; i < 3; i++)
    for (j = 0; j < 3; j++)
      eta[i][j] = 0.0;

  T::resetIntegrator();
}

template<typename T> void NPTf<T>::evolveEtaA() {

  int i, j;

  for(i = 0; i < 3; i ++){
    for(j = 0; j < 3; j++){
      if( i == j)
        eta[i][j] += dt2 *  instaVol *
          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
      else
        eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
    }
  }

  for(i = 0; i < 3; i++)
    for (j = 0; j < 3; j++)
      oldEta[i][j] = eta[i][j];
}

template<typename T> void NPTf<T>::evolveEtaB() {

  int i,j;

  for(i = 0; i < 3; i++)
    for (j = 0; j < 3; j++)
      prevEta[i][j] = eta[i][j];

  for(i = 0; i < 3; i ++){
    for(j = 0; j < 3; j++){
      if( i == j) {
        eta[i][j] = oldEta[i][j] + dt2 *  instaVol *
          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
      } else {
        eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2);
      }
    }
  }
}

template<typename T> void NPTf<T>::calcVelScale(void){
  int i,j;

  for (i = 0; i < 3; i++ ) {
    for (j = 0; j < 3; j++ ) {
      vScale[i][j] = eta[i][j];

      if (i == j) {
        vScale[i][j] += chi;
      }
    }
  }
}

template<typename T> void NPTf<T>::getVelScaleA(double sc[3], double vel[3]) {
 
  matVecMul3( vScale, vel, sc );
}

template<typename T> void NPTf<T>::getVelScaleB(double sc[3], int index ){
  int j;
  double myVel[3];
  double vScale[3][3];

  for (j = 0; j < 3; j++)
    myVel[j] = oldVel[3*index + j];

  matVecMul3( vScale, myVel, sc );
}

template<typename T> void NPTf<T>::getPosScale(double pos[3], double COM[3],
                                               int index, double sc[3]){
  int j;
  double rj[3];

  for(j=0; j<3; j++)
    rj[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j];

  matVecMul3( eta, rj, sc );
}

template<typename T> void NPTf<T>::scaleSimBox( void ){

  int i,j,k;
  double scaleMat[3][3];
  double eta2ij;
  double bigScale, smallScale, offDiagMax;
  double hm[3][3], hmnew[3][3];


  // Scale the box after all the positions have been moved:

  // Use a taylor expansion for eta products:  Hmat = Hmat . exp(dt * etaMat)
  //  Hmat = Hmat . ( Ident + dt * etaMat  + dt^2 * etaMat*etaMat / 2)

  bigScale = 1.0;
  smallScale = 1.0;
  offDiagMax = 0.0;

  for(i=0; i<3; i++){
    for(j=0; j<3; j++){

      // Calculate the matrix Product of the eta array (we only need
      // the ij element right now):

      eta2ij = 0.0;
      for(k=0; k<3; k++){
        eta2ij += eta[i][k] * eta[k][j];
      }

      scaleMat[i][j] = 0.0;
      // identity matrix (see above):
      if (i == j) scaleMat[i][j] = 1.0;
      // Taylor expansion for the exponential truncated at second order:
      scaleMat[i][j] += dt*eta[i][j]  + 0.5*dt*dt*eta2ij;

      if (i != j)
        if (fabs(scaleMat[i][j]) > offDiagMax)
          offDiagMax = fabs(scaleMat[i][j]);
    }

    if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i];
    if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i];
  }

  if ((bigScale > 1.01) || (smallScale < 0.99)) {
    sprintf( painCave.errMsg,
             "NPTf error: Attempting a Box scaling of more than 1 percent.\n"
             " Check your tauBarostat, as it is probably too small!\n\n"
             " scaleMat = [%lf\t%lf\t%lf]\n"
             "            [%lf\t%lf\t%lf]\n"
             "            [%lf\t%lf\t%lf]\n",
             scaleMat[0][0],scaleMat[0][1],scaleMat[0][2],
             scaleMat[1][0],scaleMat[1][1],scaleMat[1][2],
             scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]);
    painCave.isFatal = 1;
    simError();
  } else if (offDiagMax > 0.01) {
    sprintf( painCave.errMsg,
             "NPTf error: Attempting an off-diagonal Box scaling of more than 1 percent.\n"
             " Check your tauBarostat, as it is probably too small!\n\n"
             " scaleMat = [%lf\t%lf\t%lf]\n"
             "            [%lf\t%lf\t%lf]\n"
             "            [%lf\t%lf\t%lf]\n",
             scaleMat[0][0],scaleMat[0][1],scaleMat[0][2],
             scaleMat[1][0],scaleMat[1][1],scaleMat[1][2],
             scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]);
    painCave.isFatal = 1;
    simError();
  } else {
    info->getBoxM(hm);
    matMul3(hm, scaleMat, hmnew);
    info->setBoxM(hmnew);
  }
}

template<typename T> bool NPTf<T>::etaConverged() {
  int i;
  double diffEta, sumEta;

  sumEta = 0;
  for(i = 0; i < 3; i++)
    sumEta += pow(prevEta[i][i] - eta[i][i], 2);

  diffEta = sqrt( sumEta / 3.0 );

  return ( diffEta <= etaTolerance );
}

template<typename T> double NPTf<T>::getConservedQuantity(void){

  double conservedQuantity;
  double totalEnergy;
  double thermostat_kinetic;
  double thermostat_potential;
  double barostat_kinetic;
  double barostat_potential;
  double trEta;
  double a[3][3], b[3][3];

  totalEnergy = tStats->getTotalE();

  thermostat_kinetic = fkBT * tt2 * chi * chi /
    (2.0 * eConvert);

  thermostat_potential = fkBT* integralOfChidt / eConvert;

  transposeMat3(eta, a);
  matMul3(a, eta, b);
  trEta = matTrace3(b);

  barostat_kinetic = NkBT * tb2 * trEta /
    (2.0 * eConvert);

  barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
    eConvert;

  conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
    barostat_kinetic + barostat_potential;

  return conservedQuantity;

}

template<typename T> string NPTf<T>::getAdditionalParameters(void){
  string parameters;
  const int BUFFERSIZE = 2000; // size of the read buffer
  char buffer[BUFFERSIZE];

  sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
  parameters += buffer;

  for(int i = 0; i < 3; i++){
    sprintf(buffer,"\t%G\t%G\t%G;", eta[i][0], eta[i][1], eta[i][2]);
    parameters += buffer;
  }

  return parameters;

}
Revision:	1097
Committed:	Mon Apr 12 20:32:20 2004 UTC (20 years, 2 months ago) by gezelter
File size:	7175 byte(s)
Log Message:	Changes for RigidBody dynamics (Somewhat extensive)
#	User	Rev	Content
1	gezelter	829	#include <math.h>
2	mmeineke	857
3	gezelter	1097	#include "MatVec3.h"
4	gezelter	576	#include "Atom.hpp"
5			#include "SRI.hpp"
6			#include "AbstractClasses.hpp"
7			#include "SimInfo.hpp"
8			#include "ForceFields.hpp"
9			#include "Thermo.hpp"
10			#include "ReadWrite.hpp"
11			#include "Integrator.hpp"
12	tim	837	#include "simError.h"
13	gezelter	576
14	gezelter	772	#ifdef IS_MPI
15			#include "mpiSimulation.hpp"
16			#endif
17	gezelter	576
18	gezelter	578	// Basic non-isotropic thermostating and barostating via the Melchionna
19	gezelter	576	// modification of the Hoover algorithm:
20			//
21			// Melchionna, S., Ciccotti, G., and Holian, B. L., 1993,
22	tim	837	// Molec. Phys., 78, 533.
23	gezelter	576	//
24			// and
25	tim	837	//
26	gezelter	576	// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.
27
28	tim	645	template<typename T> NPTf<T>::NPTf ( SimInfo theInfo, ForceFields the_ff):
29			T( theInfo, the_ff )
30	gezelter	576	{
31	tim	837	GenericData* data;
32			DoubleArrayData * etaValue;
33			vector<double> etaArray;
34	mmeineke	780	int i,j;
35	tim	837
36	mmeineke	780	for(i = 0; i < 3; i++){
37			for (j = 0; j < 3; j++){
38	tim	837
39	gezelter	588	eta[i][j] = 0.0;
40	mmeineke	780	oldEta[i][j] = 0.0;
41			}
42			}
43	tim	837
44	mmeineke	855
45			if( theInfo->useInitXSstate ){
46	tim	837	// retrieve eta array from simInfo if it exists
47			data = info->getProperty(ETAVALUE_ID);
48			if(data){
49			etaValue = dynamic_cast<DoubleArrayData*>(data);
50	mmeineke	855
51	tim	837	if(etaValue){
52	mmeineke	855	etaArray = etaValue->getData();
53
54			for(i = 0; i < 3; i++){
55			for (j = 0; j < 3; j++){
56			eta[i][j] = etaArray[3*i+j];
57			oldEta[i][j] = eta[i][j];
58			}
59			}
60	tim	837	}
61			}
62	mmeineke	855	}
63	tim	837
64	mmeineke	780	}
65	gezelter	588
66	mmeineke	780	template<typename T> NPTf<T>::~NPTf() {
67	tim	767
68	mmeineke	780	// empty for now
69			}
70	tim	767
71	mmeineke	780	template<typename T> void NPTf<T>::resetIntegrator() {
72	tim	837
73	mmeineke	780	int i, j;
74	tim	837
75	mmeineke	780	for(i = 0; i < 3; i++)
76			for (j = 0; j < 3; j++)
77			eta[i][j] = 0.0;
78	tim	837
79	mmeineke	780	T::resetIntegrator();
80	gezelter	576	}
81
82	mmeineke	780	template<typename T> void NPTf<T>::evolveEtaA() {
83	tim	837
84	mmeineke	780	int i, j;
85	tim	837
86	mmeineke	780	for(i = 0; i < 3; i ++){
87			for(j = 0; j < 3; j++){
88			if( i == j)
89	tim	837	eta[i][j] += dt2 * instaVol *
90	mmeineke	780	(press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
91			else
92			eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
93			}
94			}
95	tim	837
96	mmeineke	780	for(i = 0; i < 3; i++)
97			for (j = 0; j < 3; j++)
98			oldEta[i][j] = eta[i][j];
99	tim	767	}
100
101	mmeineke	780	template<typename T> void NPTf<T>::evolveEtaB() {
102	tim	837
103	mmeineke	780	int i,j;
104	gezelter	772
105	mmeineke	780	for(i = 0; i < 3; i++)
106			for (j = 0; j < 3; j++)
107			prevEta[i][j] = eta[i][j];
108	mmeineke	778
109	mmeineke	780	for(i = 0; i < 3; i ++){
110			for(j = 0; j < 3; j++){
111			if( i == j) {
112	tim	837	eta[i][j] = oldEta[i][j] + dt2 * instaVol *
113	mmeineke	780	(press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
114			} else {
115			eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2);
116			}
117			}
118			}
119			}
120	gezelter	600
121	mmeineke	857	template<typename T> void NPTf<T>::calcVelScale(void){
122	mmeineke	780	int i,j;
123	gezelter	576
124	gezelter	588	for (i = 0; i < 3; i++ ) {
125			for (j = 0; j < 3; j++ ) {
126	tim	767	vScale[i][j] = eta[i][j];
127	tim	837
128	gezelter	588	if (i == j) {
129	tim	837	vScale[i][j] += chi;
130			}
131	gezelter	588	}
132			}
133	mmeineke	857	}
134	tim	837
135	mmeineke	857	template<typename T> void NPTf<T>::getVelScaleA(double sc[3], double vel[3]) {
136
137	gezelter	1097	matVecMul3( vScale, vel, sc );
138	mmeineke	780	}
139	gezelter	600
140	mmeineke	780	template<typename T> void NPTf<T>::getVelScaleB(double sc[3], int index ){
141	mmeineke	857	int j;
142	mmeineke	780	double myVel[3];
143			double vScale[3][3];
144	gezelter	600
145	mmeineke	780	for (j = 0; j < 3; j++)
146			myVel[j] = oldVel[3*index + j];
147	tim	767
148	gezelter	1097	matVecMul3( vScale, myVel, sc );
149	mmeineke	780	}
150	tim	767
151	tim	837	template<typename T> void NPTf<T>::getPosScale(double pos[3], double COM[3],
152	mmeineke	780	int index, double sc[3]){
153			int j;
154			double rj[3];
155	tim	767
156	mmeineke	780	for(j=0; j<3; j++)
157			rj[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j];
158	tim	767
159	gezelter	1097	matVecMul3( eta, rj, sc );
160	mmeineke	780	}
161	tim	767
162	mmeineke	780	template<typename T> void NPTf<T>::scaleSimBox( void ){
163	tim	767
164	mmeineke	780	int i,j,k;
165			double scaleMat[3][3];
166			double eta2ij;
167			double bigScale, smallScale, offDiagMax;
168			double hm[3][3], hmnew[3][3];
169	tim	767
170	mmeineke	780
171	tim	837
172	gezelter	577	// Scale the box after all the positions have been moved:
173	tim	837
174	gezelter	578	// Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat)
175			// Hmat = Hmat . ( Ident + dt * etaMat + dt^2 * etaMat*etaMat / 2)
176	tim	837
177	gezelter	617	bigScale = 1.0;
178			smallScale = 1.0;
179			offDiagMax = 0.0;
180	tim	837
181	gezelter	578	for(i=0; i<3; i++){
182			for(j=0; j<3; j++){
183	tim	837
184	gezelter	588	// Calculate the matrix Product of the eta array (we only need
185			// the ij element right now):
186	tim	837
187	gezelter	588	eta2ij = 0.0;
188	gezelter	578	for(k=0; k<3; k++){
189	gezelter	588	eta2ij += eta[i][k] * eta[k][j];
190	gezelter	578	}
191	tim	837
192	gezelter	588	scaleMat[i][j] = 0.0;
193			// identity matrix (see above):
194			if (i == j) scaleMat[i][j] = 1.0;
195			// Taylor expansion for the exponential truncated at second order:
196			scaleMat[i][j] += dteta[i][j] + 0.5dtdteta2ij;
197	gezelter	617
198			if (i != j)
199	tim	837	if (fabs(scaleMat[i][j]) > offDiagMax)
200	gezelter	617	offDiagMax = fabs(scaleMat[i][j]);
201	gezelter	578	}
202	gezelter	617
203			if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i];
204			if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i];
205	gezelter	578	}
206	tim	837
207	mmeineke	853	if ((bigScale > 1.01) \|\| (smallScale < 0.99)) {
208	gezelter	617	sprintf( painCave.errMsg,
209	mmeineke	853	"NPTf error: Attempting a Box scaling of more than 1 percent.\n"
210	gezelter	617	" Check your tauBarostat, as it is probably too small!\n\n"
211			" scaleMat = [%lf\t%lf\t%lf]\n"
212			" [%lf\t%lf\t%lf]\n"
213			" [%lf\t%lf\t%lf]\n",
214			scaleMat[0][0],scaleMat[0][1],scaleMat[0][2],
215			scaleMat[1][0],scaleMat[1][1],scaleMat[1][2],
216			scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]);
217			painCave.isFatal = 1;
218			simError();
219	mmeineke	853	} else if (offDiagMax > 0.01) {
220	gezelter	617	sprintf( painCave.errMsg,
221	mmeineke	853	"NPTf error: Attempting an off-diagonal Box scaling of more than 1 percent.\n"
222	gezelter	617	" Check your tauBarostat, as it is probably too small!\n\n"
223			" scaleMat = [%lf\t%lf\t%lf]\n"
224			" [%lf\t%lf\t%lf]\n"
225			" [%lf\t%lf\t%lf]\n",
226			scaleMat[0][0],scaleMat[0][1],scaleMat[0][2],
227			scaleMat[1][0],scaleMat[1][1],scaleMat[1][2],
228			scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]);
229			painCave.isFatal = 1;
230			simError();
231			} else {
232			info->getBoxM(hm);
233	gezelter	1097	matMul3(hm, scaleMat, hmnew);
234	gezelter	617	info->setBoxM(hmnew);
235			}
236	gezelter	576	}
237
238	mmeineke	780	template<typename T> bool NPTf<T>::etaConverged() {
239			int i;
240			double diffEta, sumEta;
241	gezelter	600
242	mmeineke	780	sumEta = 0;
243	tim	767	for(i = 0; i < 3; i++)
244	tim	837	sumEta += pow(prevEta[i][i] - eta[i][i], 2);
245
246	mmeineke	780	diffEta = sqrt( sumEta / 3.0 );
247	tim	837
248	mmeineke	780	return ( diffEta <= etaTolerance );
249	gezelter	576	}
250
251	mmeineke	780	template<typename T> double NPTf<T>::getConservedQuantity(void){
252	tim	837
253	tim	763	double conservedQuantity;
254	mmeineke	782	double totalEnergy;
255	gezelter	772	double thermostat_kinetic;
256			double thermostat_potential;
257			double barostat_kinetic;
258			double barostat_potential;
259			double trEta;
260			double a[3][3], b[3][3];
261	tim	763
262	mmeineke	782	totalEnergy = tStats->getTotalE();
263	tim	763
264	tim	837	thermostat_kinetic = fkBT * tt2 * chi * chi /
265	gezelter	772	(2.0 * eConvert);
266	tim	763
267	gezelter	772	thermostat_potential = fkBT* integralOfChidt / eConvert;
268	tim	763
269	gezelter	1097	transposeMat3(eta, a);
270			matMul3(a, eta, b);
271			trEta = matTrace3(b);
272	tim	767
273	tim	837	barostat_kinetic = NkBT * tb2 * trEta /
274	gezelter	772	(2.0 * eConvert);
275	tim	837
276			barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
277	gezelter	772	eConvert;
278	tim	767
279	mmeineke	782	conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
280	gezelter	772	barostat_kinetic + barostat_potential;
281	tim	837
282			return conservedQuantity;
283
284	tim	763	}
285	tim	837
286			template<typename T> string NPTf<T>::getAdditionalParameters(void){
287			string parameters;
288			const int BUFFERSIZE = 2000; // size of the read buffer
289			char buffer[BUFFERSIZE];
290
291	mmeineke	853	sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
292	tim	837	parameters += buffer;
293
294			for(int i = 0; i < 3; i++){
295	mmeineke	853	sprintf(buffer,"\t%G\t%G\t%G;", eta[i][0], eta[i][1], eta[i][2]);
296	tim	837	parameters += buffer;
297			}
298
299			return parameters;
300
301			}